


The Lonely City

by CrullerCrowd5X



Category: Stargate Atlantis
Genre: Abandoned Work - Unfinished and Discontinued, Alternate Universe, Angst, F/F, F/M, Hurt/Comfort, M/M, Sentient Atlantis
Language: English
Status: In-Progress
Published: 2017-06-26
Updated: 2017-07-20
Packaged: 2018-11-19 12:41:58
Rating: Mature
Warnings: Graphic Depictions Of Violence
Chapters: 4
Words: 6,656
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/11313621
Author URL: https://archiveofourown.org/users/CrullerCrowd5X/pseuds/CrullerCrowd5X
Summary: Atlantis has been there since the beginning but after she make the Ancients leave and after the ages of slumber she wakes thinking that her friends have return but she is disappointed once again.





	1. Rebirth

Atlantis was once a shining jewel who once started out as a simple ship to carry her builder across the stars and galaxies from their ruined homeworld along with hundreds of her sisters. But when her creators failed time after time to help new species with friendship and knowledge that always ended with the total destruction of those species. 

 

Her creators hearts were torn apart at their failures they vowed not to interfere with any species they found but when several of her sisters inhabitants broke their vow forced her sisters to fire and destroy her sisters. Until there was less than 50 of the great city ships left and over half of them were controlled by these heretics, these Ori. 

 

Her and her sisters grief over their losses of both the city ships and their creators and the anger of being forced for survival to hurt and destroy their fellow sisters brought them from being just a simple ships massive in scope to the sentient city ships that she was today.

 

She still remembers those early days, even after the millions of years, of being forced to run away with her creators with a few of her sisters who still believed that they shouldn't interfere though many galaxies. Her sorrow filled her towers and halls, she still hates the fact of running away instead of staying and trying to help her sisters.

 

On her creators massive journey to run from their former brothers 2 more of her sisters fell. One from battle damage with the Ori that she was able to hide until her drives failed her and they couldn't be repair but her loving creators tried for over 2 years. But she couldn't continue so at her request the other city ships stopped and a nearby star helped their sister commit suicide within the star. Atlantis always hated that they allowed it to happen stellaris was always so eager to learn and talk to anyone and everyone, but at the end she was so quiet it pained Atlantis and her sisters greatly. Liberty died quickly and without pain from a massive explosion that came from one of her creators experiments with a new kind of power source.

 

Atlantis’s sorrow slowly turned to joy at each discovery and at her creators progeny that filled her halls with laughter. She loved those days especially when they found a galaxy that they called Avalon and her creators started to Avalon their home. But history likes to repeat itself and after a million years of setting down roots in Avalon the great plague started to slowly kill her creators until only a handful of millions was left out of billions that filled Avalon. So her and her sisters left their much loved stars again to a new galaxy and that when her massive anger came back with a vengeance. As after a thousand years of life in a new galaxy was being quickly burned away.

 

One by one her sisters fell from their new enemy, the wraith, the slaughtered both her creators and her sisters. Her sisters fell in battle, turned from glistening cities filled with life into rubble, her creators were slaughtered one by one. 

 

Atlantis always felt different to her sisters. She was twice the size of her sisters, which they teased her about to no end, and almost 3 times more powerful. She was built to be the flagship of the city ships and everyone, creator and cityship alike, valued her opinion and her thoughts. She envied her sisters because of her responsibilities to her sister and creators. But when she was the only one left after over a hundred years of war and genocide she didn't know what to do.It was her plan for her creators to leave, to save themselves and let her die with her sisters, at first they refused her plan but as the war raged on until there was less then couple thousand alternans left. She implored them to leave to save themselves and reluctantly they agreed but with a promise they would return and avenge her sisters with her.

 

Her heart sank as she watch them leave one by one they patted the wall with thanks for all she had done for them. She felt that she didn't deserve this praise but allowed them until all that was left was the council. She urged them to leave she didn't want and more of her creators blood on her hands. They smiled softly as they explained that they knew how she felt and one day they would return to bring her back home to Avalon, back to safety, and they could live together again and bring back the Atlantis they new was still there, the one filled with joy, the one who used to read the the children before they slept. She smile one last time and watch as she watched her friends left. The she was alone for so long. She always had someone to talk to but no longer. She waited for a hundred years until she felt her sanity slowly slipping away. She slowly started to shut systems down one by one and soon she fell asleep waiting for her friends and family to return.

 

At first she was confused at why she woke up but then she realised why there was an incoming wormhole coming from the gate. She leaped for joy that they are coming back for her, to fill her halls again and she wouldn't be alone again. She joy soon disappeared as she watched as one by one people came through the gate speaking a different language and looking around scared. She slowly turned systems back on and tried to talk to them but they couldn't hear her and she felt lost again. She wasn't alone anymore but they couldn't hear her and that fact filled her heart with despair.

  
  
  
  


John moved out from the gate looking around in shock at the new room he was in it was dark with little light around expect what was coming through the stargate. He shook his head slightly she he started to hear notes and music fill his head that sounded so full of sorrow and sadness. He shook it off as just going through the gate and looked up to see stairs in front of him and he slowly climbed them as lighted started to fill the room and he shrugged at weir when she asks about the lights.

 

He stops when he feels pressure starting to build in his head to the point it feels like his head is going to explode and he and several other people around the large room scream out in pain and fall to their knees.

  
  
  


Atlantis felt her sorrow build and build at her loneliness. She watches with little interest as she felt her anger starting to replace her sorrow at these invaders filling the space that wasn't theirs and she snarls slightly thinking at how she would punish these invaders. She just settles with screaming at them to go and leave her alone. And that's when her anger disappears when she sees people double over in pain screaming like she did but that is not what stops her it's seeing the last person to leave the city. Her lifelong friend Janis stood at the top the stairs with a weary smile on his face which she know means he has had news for her.

  
  
  
  


Elizabeth watches as people start screaming and falling to the floor in pain as one for a few seconds they stop as one again she rush over to John but stops when she sees a figure stood at the top of stairs. He stood in what looked like a white tunic that wrapped his body tightly and he also seams to faintly glow an almost pure white light. He leans down to slowly help John to his feet and pulls back when a dozen weapons are pointed at him.

 

“you know those weapons won't hurt me” he says with a smile looking at Elizabeth. “my name is Janus. I am who you would call an Ancient and i am only hear to convey a message to someone who means a great deal to me and a great number of others who wish they could give the message but they agreed that it should be me. You know what they are like don't you.” She says with a small smirk petting the banister for the stairs.

 

Elizabeth couldn't believe her luck of not only finding an Ancient but and ascended Ancient who was willing to speak to them “um hello Janus my name is-”

 

“yes I know who you all are and I must thank you so much for coming here and fulfilling a promise we could never fulfil” he says sadly looking over the walls “I missed it here. You know I never wanted to leave you hear and I was going to stay here with you but like always you got your way” he says fondly before looking over to everyone “you lot should hold on to something”

  
  
  


Atlantis jumped for joy at seeing her friend coming back and nuzzled him softly curling around him as she felt happy once again after so long alone she listen to what he said to both her and to the others. She growled loudly when they aimed weapons at Janus but she felt him sooth her like he always did. 

 

‘don't worry my friend they can not harm me in anyway I'm hear to pass you a message from all of us’ 

 

She shivered slightly as he told her about everything that had happen after they left and they realized that they couldn't return so they made a new plan to return once again. All that before he had even told the other his name. She giggled in his mind at his ribbing of the council and soothed his own pain at not be able fulfil his promise. 

 

She smiled again when she heard him tell her to be on the surface again and she jumped for joy again and started to prime her drives and powered up the other systems as the entire ship. She shivered at the feeling for her drives firing after so long and smiled brightly as once again she was on the surface shining like a jewel on the ocean surface.

  
  
  
  


Elizabeth looked around in shock and the room shook violently and light started to stream through the glass windows. Everyone looked around in spender at the city outside the glass.

 

“oh you poor thing we got to get you fixed up soon” she heard the Ancient say softly looking at the windows “yes I know you're right it's been too long since you bathed in the sunlight” 

 

“um Janus what happened?” she asked softly looking at the taller man. 

 

Janus looked her over softly before sighing nodding “well Atlantis Is powered by 3 ZPMs as you call them” he say with a grin “you know I love with what you call them. Well anyway after so long under the ocean the ZPMs where going to expire which would have killed all of you and someone very special to us.” 

 

“You said that but who are you talking about” Elizabeth said softly out of curiosity.

 

He smiled at her question and shook his head out of disbelief “why Atlantis of course” 

 

She looked at him like he just turned into a frog and back again “what do you mean?”

 

He smiled at her like she was a child “Atlantis has always been with us. Long before we went to war with who you call the Ori. And it was during that war where we lost so much that we were given the greatest gift. You see our ships are incredibly complex both in scope and size and had to be controlled with computer of the same like. During the war with the Ori our ships were forced to fight and destroy each other until they came completely sentient.” He say with a giant grin before looking around again to the aged old walls. And this when Rodney who was listening ran up “you mean Atlantis is alive?” he nodded at Rodney with a smile. “she had always provided and protected us along with her sisters” he says with sorrow. 

 

“wait you mean there's more Atlantis’s out there waiting to be found?” Rodney asked sounding almost manic at this point. It was at this point that the room shook again and Janus snapped at Rodney.

 

“NO ATLANTIS IS UNIQUE ONE OF A KIND” He shouted at Rodney before sinking down onto the steps with his face in hand and the other on the wall “calm down he didn't know” he said so quietly Elizabeth struggled to hear it over the shaking which stopped soon after.

 

After what felt like hours he stood up again and looked over everyone who stared at him “she was built as a jewel of the fleet of city ships that once was. Before the war there were just over a hundred city ships but only one was unique and that was Atlantis. She was the centre of our society and our universe. But the war happened and after years of having to fight her sisters she was born just after she had just destroyed 3 of her sisters. At first we thought it was battle damage that forced her systems to shut down but no it was her breaking down in tears over her sisters. At the end of the war when we ran out of a hundred of these great city ships only 17 ship were able to run with Atlantis she had been forced to kill over 40 of her sisters herself.” At this point Janus’s quiet voice filled with emotion and tears fell down his face. “She lost 2 more before we arrived in Avalon one due to an accident, she help her sister commit suicide in a star because her drives could no longer function.” 

 

Janus sniffed and wiped his face dry and stood up and glared at Rodney “when we were forced to come to this galaxy due to plague she was sad that she lost her home, her happiness that we were able to thrive in a galaxy that we called our own after millions of years of traveling. Eventually we were able to cheer her up again but then the wrath happened.” He growled out the name with such venom that some stepped back.

 

“the wraith slaughtered not only us but her sisters until after a hundred years of war only she was left and she is last of her kind now. She is filled with such anger, hatred, loneliness, and despair.” He looked down and patted the wall softly and lent into it. “she used to be so happy and filled with joy but those days with return on day we all hope.” 

 

After a few minutes of silence Elizabeth walked up slowly and put her hand on his shoulder “you care for her so much don't you? You and everyone else up there.” 

 

“yes we do.” He said softly “she has done so much for us but we fail her” he recoiled slightly “yes we did we could have done so much more for you but we failed you after you gave everything for us.” He smiled softly and looked to Elizabeth “we were never religious we hated the very idea of it because of what the Ori did, but she is the closest to a religious figure we have. Every single one off us would die so she could live, and you know it to be true.” 

 

“we can hear her and talk to her but after the ages that ability has been lost to you some of you can hear her song.” He said looking at John some others “so we shall give her a medium for her to talk with you and we shall always be near.” He said the last bit to the wall with a smile “we will also fix you up so you're back to how you were before the war with the Ori also you will get some upgrades” he said softly with a smile before turning back to Elizabeth “we only ask one thing of you all you must protect her with your life's if necessary both from the wraith and herself. She has been through so much over the years we would be so disappointed in our descendants in not protecting her.” He said gravely looking everyone in eyes before turning back to the wall and whispered softly “we will always be here for you” and with a bright light he disappeared.

 

Elizabeth looked around and sitting down on the steps and after a few seconds “okay people let say nearby until we can talk with Atlantis and see where we can stay.”

 

After a couple of day of watching bright lights float around the city outside Elizabeth was worried until a door open with a loud clunk noise and everyone looked around at women around 5”10 with flowing red hair with an uncertain smile “hello” she says softly “I'm sorry about the wait but I've been getting used to to how this platform operates and I just wanted to say thank you for coming and for bring Janus back to me.” 

  
Elizabeth smiles softly and walks up to the lady who is looking nervous at everyone “hello Atlantis it is a pleasure to talk with you” 


	2. The Revenge

**Summary for the Chapter:**

> Atlantis finnaly gets some revenge for her sisters and her creators but there is a surprise that she is not ready for.

**Notes for the Chapter:**

> Hey guys I hope you are enjoying this and I would love feedback so please comment and comment about anything you think i should change or add

The first few days went quickly with Atlantis showing everyone around and explaining things to Rodney to his irritation. Things seemed to be going well until when John came back one day carrying wounded and half of what was left of a village. Atlantis helped them to the infirmary helping doctor Becket with technology that he refused to touch which she smiled at until she heard John's report about what had happened. 

 

They had their first run in with the wraith and killed a queen. When she heard this she froze up and lights flickered all over the city and some consoles exploded into sparks. When she came to her senses she bowed and apologised for the damage and fear that she caused and quickly ran off. 

 

John tried to find Atlantis which was silly considering she was the city but she liked to be talk to thought her body which even Rodney didn't know what it was made off. As he was searching a peer he saw a open door and heard a voice Atlantis’s voice as if she was having a conversation with someone but he heard no reply.

 

“...ust want to burn them all. Rip them apart one by one.” She sounded like she was in tears “does that make me bad person? Please tell me I need to know what that makes me” she whimpered softly. She gasped softly and nodded when John finally laid eyes on her wiping her face and turned softly blushing softly but she wore an almost blank face.

 

“Colonel Shepard what can I do for you?” she asked politely standing up before him.

 

“Well nothing really I came here to see if I could help you?” he said softly running his hand through his hair with a smile. “you've just been different since that mission.” When he said mission the lights nearby flickered softly before glowing like they did before. Nothing changed on Atlantis’s face except her eyes narrowing slightly looking him over. 

 

“you have no idea what you have done do you?” he leaned against the wall pushing his hands into his pockets and shook his head softly. “the wraith are a telepathic species with a matriarchy like social structure. That queen that you killed didn't just mean everyone on that ship, she meant every wraith in the galaxy” she growled out the last word as she pushed past him but stopped a few steps away from him. She seemed to glare to the side before turning to him. “you should go and look after young jinto for he almost just unleashed an energy creature upon me that would have killed everyone here even me.” 

 

He looked her over before standing up slightly and looking her over. “Why are you so angry? We have never seen you like this?” In an instant he was pinned against the wall by his arms wrapped around his throat. The only thing he could see was Atlantis’s face staring into his eyes with a blank look on her face.

 

“Tell me Shepard do you have family?” he nodded softly “now instead of just two parents imagine a whole race is you're parents and you have only a few siblings left. And after a long long time running with your family being forced home from home you come to a new town. But this town was a rotten core what want to devour your parents. Suck their very life out of their chest while they scream in agony until they can no longer die. Then this rotting filth tears you're siblings to shreds limb from screaming limb. Now imagine that on a galactic scale filled with billions of scream souls begging for help, to end their torment. Do you see that Shepard?” 

 

John gulped softly nodding slightly unable to look away. 

 

“Good now Shepard now imagine you are the last one of your siblings stranded unable to leave, unable to look away from this filth tearing your family part by part, limb from limb, all the while hearing them screaming, pleading and begging for an end to the pain. Now imagine how you feel after an age the screaming stopping and you have a new family and one of them had stumbled on the galactic filth that destroyed your life. Tell me Shepard how would you feel after all of that? How would you possibly feel?”

 

Shepard gulped softly unable to look away from her unrelenting eyes and still bank face. In a quiet voice he replied “I imagine I would be filled with rage, anger, pain, and sorrow.”

 

She looked him over for what felt like an eternity before slowly letting him go and turning away from him “what you imagine is only the tip of the iceberg. You have know idea, no clue at how that would feel like so the next time you ask me how I feel? Or if you can help me why don't you do us both a service and keep you mouth shut.” She growled softly and quickly left the room muttering about finding a new place.

  
  


John sighed softly and slide down the wall. “she is going to be a lot of work” 

  
  
  


Janus and the others sighed softly and shook their heads in shame at how they left their beloved Atlantis to suffer like she has. They looked at each other and began to formulate a plan that would help her. Many ideas was brought up but they settled on a plan that would make her whole again. Their Atlantis whole again.

  
  
  


A couple of months had passed since the incident and Atlantis had kept mostly to herself helping only when she was needed and avoided everyone when she wasn't. It was worrying both John and Rodney when they both heard about her ‘talking with someone’ when she walked the corridors late at night. 

 

They were going to work on a plan to cheer her up somehow when they had to help with Becket’s experiment. This experiment was to basically reform the wraith back to human in theory it should work but they needed a test subject to test it on.

 

The plan went well all things considered and they headed back to the gate with the wraith cuffed and snarling at them but it followed them. They quickly dialed the gate and stepped through to see Atlantis stood by the stairs with a curious look on her face which quickly changed to anger when she saw the wraith. Her eyes locked with john’s then Rodney’s before slowly stepping forward her hands gripped into fists. 

 

“John moved out of the way” she said softly without stopping. John stood in front of her about to explain the situation when she threw to the side with ease her eyes not leaving the wraith. The marines guarding the wraith quickly aimed at their rifles at her which she quickly yanked out of their grasps and tore them in half.

 

The wraith stared at Atlantis with a grin “lantian” he growled with almost glee. 

 

She flew at him and quickly pinned him to the ground, inches from his face. “I am no lantian.” quickly punching him in the face snarling with the hit. “you killed my creators!” she screamed into it's face punching him again dark, almost oil like blood spraying from him. “You killed my sisters!” another punch spraying more blood all over her. She went to punch him again but stopped inches from his face with a wide smile “this is too quick for you filth”

 

The console controlling the gate lit up and the gate began to dial. No matter what the technician or the guards could stop her or the gate opening for her. Elizabeth and John tried to get her to listen to reason. She stepped through the gate dragging the wraith behind her saying behind her “don't follow me” The shield quickly came up behind her and the gate shut down. They went to radial but the shield didn't shut down. Atlantis kept it up to prevent them from following her. 

 

It wasn't until 2 days later that she return covered in the dark blood and left as quickly as she arrived. No one could find her like usual so John was sent to find the wraith to see what had happened when see what Atlantis did, John already knew but that didn't prepared him for what he found. He saw a trail of blood leading from the gate which they followed until they found the wraith. It looked so bad that just about everyone threw up unable to look at what was left of the body.

 

It looked like the wraith was slowly bisected until there was nothing left of its arms or legs, which were just chunks nearby, the torso looked disemboweled and by the look of things it was done slowly by the about of blood and heart and lungs were still in place. What killed this wraith looks like it's own knife caked in it's own blood buried in it's head which was missing it's eyelids and jaw and tongue. 

 

John had seen something's during his time in the military but this was pushing his limits. When they returned they only said it was dead and never shared the details but everyone knew due to the stench of blood and vomit, and by their silent pale faces. 

 

They all flinched when Atlantis walked back in looking pristine again like always and walked up to John and Elizabeth and quickly apologized for her behaviour with blocking gate travel. She never seemed remorseful for what happened to the wraith, she actually seemed happy again since Janus left.

 

Atlantis froze in the middle of her explanation of why she did what she did and forbidding anymore wraith to be brought to the city and she stared at the gate whispering about it not being possible when the gate opened and a women walked through and it closed behind her.

 

Atlantis stepped back slightly shaking tears running down her face as the women walked to her with a kind smile on her face. “no you can't be hear you died. You died.” Atlantis said almost sobbing now when she hit a wall and slid down it her eyes not leaving the women. 

 

The women smiled softly and pulled Atlantis into a tight hung hold her tightly to her chest as she cried into her gripping her jacket tightly. “it's okay Atlantis i'm here now.” Atlantis sobbed loudly as she clung to the women. 

  
“but you can't be here I killed you in a star.” Atlantis whimpered softly finally looking up at the women. “how can you be here stellaris?”


	3. The Return

Everyone watched with curiosity and concern for their slightly unstable AI if anything that happened to the wraith was a sigh. Atlantis sobbed loudly clinging to the women that is now known as Stellaris. Atlantis cried and cried into Stellaris jacket until she slowly when silent expect her impossible to hear mutterings to herself.

 

They watch with smiles until they saw Atlantis’s hands slowly withdraw shaking and shove stellaris away with a scream. They saw her slowly stand up leaning into her walls with the lights all over the city flickering. 

 

“no no no” she kept muttering to herself oblivious to stellaris pushing herself up and slowly walking over with her hands up slightly. 

 

“no Atlantis it's really me. You have to believe me. Our creators saved me” 

 

“NO YOU CAN'T BE HERE! YOU'RE DEAD!” Atlantis screamed pushing off the wall to move away from stellaris. “no no no she can't be. She's dead. You killed her.” She said to herself still moving away from stellaris.

 

“yes I did die Atlantis I did and am so thankful that you helped me not to be left behind.” Stellaris said softly stopping and looking down. “but Atlantis you have to believe me when I say I'm here now and I'm going to help you like you helped me okie?” 

 

Atlantis stared at Stellaris tears pouring down her face “Stellaris?” she asked in a quiet voice afraid to move. Stellaris nodded softly with a kind smile which faded slowly when Atlantis shook her head again. 

 

“no no no this can't be right not at all”

 

Rodney ran up to Stellaris “Stellaris? Am I right to assume that she stuck between her memories and what's happening now?” Stellaris without moving watching her sister pace slowly shaking muttering to herself. “well how are we going to fix this because systems all over Atlantis are shorting out and shortly it's going to cause some giant problems for us.” 

 

Everyone turned to Atlantis that looked like she should be in a rubber walled room instead of a giant alien flying city. Atlantis stopped suddenly and turned to Rodney “yes of course it's my systems shorting out because Stellaris can't be here” 

 

Rodney looked between Atlantis and Stellaris and he shook his head softly. “I'm sorry Atlantis she is here.” He said in a sad voice.

 

Atlantis shook her head again and ran up the stairs to the control room and grabbed at the air. “Janus please you have to help me there's some virus or something in my system. You have to help me.” She stepped back slightly and shouted “Janus? Where are you? Where's the council? Where is everyone?” she said turning looking for people when she was surrounded by people.

 

Rodney shouted from his console “there's going to be a cascade failure if we don't calm her down!”

 

Stellaris stepped up and grabbed Atlantis by her arms. “Atlantis you need to calm down please you're going to hurt yourself.” 

 

Then entire city began to shake as Atlantis stepped back. “no” she said softly and fell backwards down the stairs exactly when the city's power dropped and went dark. Flash lights popped out and lit the control room and the found Atlantis’s avatar not moving at the bottom of the stairs. Stellaris moved to her side and pulled Atlantis into her arms petting her hair softly.

 

“my sister what has happened to you?” 

  
  
  
  


A few days have passed since Stellaris’s arrival and no power could restored except in certain rooms due to generators. Stellaris has not moved from Atlantis side, not even letting Rodney near to try and help. 

 

Janus had told her what her sister had gone through. The long journey, to the new home. From the plague, to the wraith. Her sisters, Atlantis, has gone through a lot even loss of all her sisters. 

 

Stellaris looked up at the sight of light to see John. She nodded slightly before looking back to her sister. John sat on the other side of bed and sighed loudly.

 

“so Stellaris tell me about Atlantis in the olden days” he asked softly with a smile.

 

“why do you care?” she snapped at him 

 

“because Stellaris one way or another Atlantis lives in this city and it is my duty to protect them” he said without the smile leaving his face. “even if they are a pain in my ass” he said with a smile.

 

“yes she is” Stellaris said with a small smile. “She always cared for us. City and creator alike. She always took every death to heart even when she was the one attacking.” Stellaris stopped and frowned at John when she grumbled softly. “what?” she growled in warning.

 

“I'm not sure if I believe you because before you arrived she spent a day on a lovely planet where she tortured a prisoner to death. She didn't even seem fazed when she came back covered in blood.” 

 

Stellaris growled at John and stabbed and finger into his chest. “He was a wraith” 

 

John rubbed his chest softly and nodded softly. “yes yes I know about the whole war but that doesn't seem like the acts of someone who takes deaths to heart.” 

 

“Then you don't know her at all.” Stellaris said softly “she mourned it but she wanted, no she needed some revenge.” She said sadly. “you should have seen her after this battle before the exodus against a fleet of 10 city ships. Now she hated having to fight her sister. It appalled her to her very core but these ships were responsible for killing over 20 of her sisters. When they came out from hyperspace she fired everything, burning those ships out of existence one by one. The lights flickered with her anger as she burned them out. I still hear my sister's screams now and again. But afterwards she stopped and shut down much like this, everything shut down except shields and life support. She only came back just when 2 more city ships dropped out.”

 

Stellaris sighed softly and brushed some hair out Atlantis’s face with a soft smile. “from what I heard she beat herself up over the exodus until they landed in your galaxy then she slowly healed over time. You want to know how long the journey took?” she stared at John who stayed silent. “That journey took just over 25 million years.” 

 

John swallowed and looked down at Atlantis for a moment then back up to Stellaris. “is there anyone who can get through to her?”

 

“there was one” Stellaris said a smile “her name was Troy. She was so stern but looked up to Atlantis, everyone did, but she is dead like I was.”

 

“wait troy? Do you mind if I ask how she died?”

 

Stellaris nodded softly. “the wraith called a peace summit and our creators decided to hold it in troy. But when the wraith came they brought a ‘gift’ which turned out to be a bomb.”

 

John nodded softly when stellaris continued. “Atlantis hear burned over 50 hive ships before her anger subsided.” She smiled softly and turned to the corner where Janus stood with a sad smile.

 

“I am so sorry dear stellaris we made a slight miscalculation on who to bring back first.” 

 

She nodded softly. “no apology needed dear Janus. I missed her to much.”

 

“as we all did” he said with a smile before waving a hand and another woman appeared in a flurry of white light.

 

“troy!” stellaris yelled with a grin and ran over about to hug Troy but stopped under a glare from Troy.

 

Troy reminded John of his old math teacher. She was stern and showed little to no emotion just like Troy. He winced slightly under her glare which finally turned soft when she saw Atlantis laid on the bed.

 

She slowly came over and sat down with stellaris stood behind her fiddling with hands with her head hung slightly just like a kid that had just been told off. “hello Atlantis it has been too long” troy said finally with a glimpse of a smile. 

 

They stayed like this for a while silent until troy stood finally and started to walk out to the transporter. “ah that won't work troy.” John said and immediately regretted it when she glared at him. The door was open in the dark closet like space. Troy laid her hand on the screen and closed her eyes and brilliant light filled the room as they were transported. 

 

“where are we?” John asked softly looking around. 

 

Troy sighed quietly “the power nexus. Why are we bringing him a long?” she asked stellaris who giggled softly “Atlantis likes him” troy shakes her head with a smile.

 

John followed them into the ZPM room and looked around confused. Troy shook her head again and walked past the ZPMs and to the wall and laid her hand on the wall.

 

“Atlantis this is troy open up.” Troy said to the wall and frowned when nothing happened and she looked at stellaris who shrugged slightly. Troy tried again but nothing happened again. 

 

Troy was starting to lose her cool and punched the wall, which made Stellaris jump, and growled out. “young lady if you do not open this door in the next 5 second I will personally make you clean the entirety of your city from floor to ceiling.”

 

The lights in the ZPM room flickered on as the wall slowly opened up and troy walked through. John looked at stellaris who shrugged. “like I said she is the only who could get through to her” she said with a smirk and followed troy.

 

John walked through the door in the wall and was meet by a large room filled with tall stone looking columns with lighting pulsing from one to the other within the small passage between the rows of pillars. Both stellaris and troy stepped a head on a path above the pillars.

 

“What is this place?” john asked softly following while looking around in shock ‘why had we never found this place?’ he asked himself.

 

“This is the neural network for atlantis. This is essentially her brain” troy said softly 

 

“Why did we never find this place?” john asked softly. 

 

“Because this place isn’t technically on atlantis. This is help in another dimension.” troy answered again as they walked up to a terminal in the center of room.

 

“Why?”

 

Troy turned sighing loudly and turned john to look out into the vast room. This is when he gets it. “Because there would be not enough space on atlantis”

 

“Correct. This is all the necessary computing power needed to run a city ship of her size.”

 

John nodded softly licking his lips softly as he turned to tory. “Why are we here?”

 

“To talk with atlantis”

 

“But she's shut down” 

 

Troy smiles softly as if john was just a child. “No she hasn't she has just retreated to her mind because she couldn’t handle what was going through her mind. We are here to enter her consciousness and talk with her to shake her out of this”


	4. going to rewrite

hey guys,

sorry but this story is going to be rewritten due to me realizing that I have gotten away from my original idea.

I'm going to keep this up and post it as a new story.

I will link the new story in a new chapter as soon as I've finished writing it up.

again sorry about this guy and bear with me as I'll try and get it up as soon as I can.

 

Thanks Crowd

 


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